Plot hole: When the aliens kidnap the adults, the kids are left behind. But all the kids seen are around 11 and younger. Where are the teenagers or young adults? None of them are during the celebration scene nor in the arena on the alien planet.
Plot hole: The movie is based in 1986 after the group time travels from 2010. That makes it a 24 year trip back in time. It is stated that Jacob is 20 years old. That is an error as this would make him roughly around 23 or 24 if he was conceived in 1986, which we saw near the end of the movie.
Suggested correction: This mistake has already been corrected. Cusack could have simply generalized his age when he mentioned it, probably not remembering his real age at the moment.
Plot hole: When Gawain is repairing the hole in the vault wall, a security camera is visible in the top corner in the room.
Plot hole: Cindy manages to pick Crisp out of a line-up even though she was hidden in a box and didn't see him, she only heard his voice. But even with that, he isn't asked to speak during the line-up.
Plot hole: In the opening of the film, some of the characters are flipping through a scrapbook they've made documenting Elle's experiences in the first film. The problem is that many of the pictures are of moments when no photos were taken, so how did they get the pictures to put in the scrapbook?
Plot hole: In the scene where bad cop says "security cameras picked up this" it shows the footage of Emmet "convulsing with the strange piece." If they had cameras down there, then they would've already found the piece of resistance. (00:08:10 - 00:10:10)
Plot hole: When the students are breaking into ETS, they take great care to avoid the security cameras in the lobby; donning masks, crawling on the ground, etc. Yet a bit later, two of them go back to guard the same lobby, they are seen walking around and sitting on the desk that they so carefully crawled past earlier.
Plot hole: The Hillbillies take a "short cut" to catch up with the guys after they are taken in by Burt Reynolds. However, the guys get a chance to sleep comfortably until morning before being confronted by them. (01:12:10)
Plot hole: It takes less than 3 minutes to fill the house with water using a mere garden hose? I mean come on...
Plot hole: Michael McKean quits pursuing Beldar and approximately 15 years pass as indicated by Connie growing up, yet when you see McKean again and his assistant, they have not aged at all.
Plot hole: The policeman survives a frontal crash into the hillbilly's truck at full speed without as much a scratch. (00:24:40)
Plot hole: While planting the suicide gear in the bathroom before Buckley comes in, Cooper tells Josh to tie the rope into a noose as they go to hide in the shower. Josh replies that he doesn't even know how to tie a noose. He must be a quick study, because in the 45 seconds or so that it would have taken Buckley to relieve himself and wash his hands, Josh has tied a perfect noose. (01:03:55)
Plot hole: The kidnappers initially ask for a ransom of $50 million. $20 million in $20s, $20 million in $50s, and $10 million in $10s. This translates to a grand total of 2.4 million bills (pieces of paper, that is) Every bill of American currency is 2.61 inches wide, 6.14 inches long, and .0043 inches thick. This makes roughly 2,791 bills to form a 1 foot tall stack. This means that the 2.4 million bills would take up a space of 96 cubic feet (assuming they are packed as tightly as possible). Also, since 490 bills make 1 pound, the 2.4 million bills would weigh (interestingly enough) just over 2.4 tons. No way they can move it.